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Wang S, Ballard TE, Christopher LJ, Foti RS, Gu C, Khojasteh SC, Liu J, Ma S, Ma B, Obach RS, Schadt S, Zhang Z, Zhang D. The Importance of Tracking "Missing" Metabolites: How and Why? J Med Chem 2023; 66:15586-15612. [PMID: 37769129 DOI: 10.1021/acs.jmedchem.3c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Technologies currently employed to find and identify drug metabolites in complex biological matrices generally yield results that offer a comprehensive picture of the drug metabolite profile. However, drug metabolites can be missed or are captured only late in the drug development process. This could be due to a variety of factors, such as metabolism that results in partial loss of the molecule, covalent bonding to macromolecules, the drug being metabolized in specific human tissues, or poor ionization in a mass spectrometer. These scenarios often draw a great deal of attention from chemistry, safety assessment, and pharmacology. This review will summarize scenarios of missing metabolites, why they are missing, and associated uncovering strategies from deeper investigations. Uncovering previously missed metabolites can have ramifications in drug development with toxicological and pharmacological consequences, and knowledge of these can help in the design of new drugs.
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Affiliation(s)
- Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - T Eric Ballard
- Takeda Development Center Americas, Inc., 35 Landsdowne St, Cambridge, Massachusetts 02139, United States
| | - Lisa J Christopher
- Department of Clinical Pharmacology, Pharmacometrics, Disposition & Bioanalysis, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, New Jersey 08543, United States
| | - Robert S Foti
- Preclinical Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Chungang Gu
- Drug Metabolism and Pharmacokinetics, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shuguang Ma
- Drug Metabolism and Pharmacokinetics, Pliant Therapeutics, 260 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - R Scott Obach
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Simone Schadt
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacher Strasse 124, 4070 Basel, Switzerland
| | - Zhoupeng Zhang
- DMPK Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Boyce M, Favela KA, Bonzo JA, Chao A, Lizarraga LE, Moody LR, Owens EO, Patlewicz G, Shah I, Sobus JR, Thomas RS, Williams AJ, Yau A, Wambaugh JF. Identifying xenobiotic metabolites with in silico prediction tools and LCMS suspect screening analysis. FRONTIERS IN TOXICOLOGY 2023; 5:1051483. [PMID: 36742129 PMCID: PMC9889941 DOI: 10.3389/ftox.2023.1051483] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Understanding the metabolic fate of a xenobiotic substance can help inform its potential health risks and allow for the identification of signature metabolites associated with exposure. The need to characterize metabolites of poorly studied or novel substances has shifted exposure studies towards non-targeted analysis (NTA), which often aims to profile many compounds within a sample using high-resolution liquid-chromatography mass-spectrometry (LCMS). Here we evaluate the suitability of suspect screening analysis (SSA) liquid-chromatography mass-spectrometry to inform xenobiotic chemical metabolism. Given a lack of knowledge of true metabolites for most chemicals, predictive tools were used to generate potential metabolites as suspect screening lists to guide the identification of selected xenobiotic substances and their associated metabolites. Thirty-three substances were selected to represent a diverse array of pharmaceutical, agrochemical, and industrial chemicals from Environmental Protection Agency's ToxCast chemical library. The compounds were incubated in a metabolically-active in vitro assay using primary hepatocytes and the resulting supernatant and lysate fractions were analyzed with high-resolution LCMS. Metabolites were simulated for each compound structure using software and then combined to serve as the suspect screening list. The exact masses of the predicted metabolites were then used to select LCMS features for fragmentation via tandem mass spectrometry (MS/MS). Of the starting chemicals, 12 were measured in at least one sample in either positive or negative ion mode and a subset of these were used to develop the analysis workflow. We implemented a screening level workflow for background subtraction and the incorporation of time-varying kinetics into the identification of likely metabolites. We used haloperidol as a case study to perform an in-depth analysis, which resulted in identifying five known metabolites and five molecular features that represent potential novel metabolites, two of which were assigned discrete structures based on in silico predictions. This workflow was applied to five additional test chemicals, and 15 molecular features were selected as either reported metabolites, predicted metabolites, or potential metabolites without a structural assignment. This study demonstrates that in some-but not all-cases, suspect screening analysis methods provide a means to rapidly identify and characterize metabolites of xenobiotic chemicals.
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Affiliation(s)
- Matthew Boyce
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | | | - Jessica A. Bonzo
- Thermo Fisher Scientific, South San Francisco, CA, United States
| | - Alex Chao
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Lucina E. Lizarraga
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Laura R. Moody
- Thermo Fisher Scientific, South San Francisco, CA, United States
| | - Elizabeth O. Owens
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Grace Patlewicz
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Imran Shah
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Jon R. Sobus
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Russell S. Thomas
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Antony J. Williams
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Alice Yau
- Southwest Research Institute, San Antonio, TX, United States
| | - John F. Wambaugh
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States,*Correspondence: John F. Wambaugh,
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Smith DA, Obach RS. Metabolites in safety testing (MIST): considerations of mechanisms of toxicity with dose, abundance, and duration of treatment. Chem Res Toxicol 2009; 22:267-79. [PMID: 19166333 DOI: 10.1021/tx800415j] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In previous papers, we have offered a strategic framework regarding metabolites of drugs in humans and the need to assess these in laboratory animal species (also termed Metabolites in Safety Testing or MIST; Smith and Obach, Chem. Res. Toxicol. (2006) 19, 1570-1579). Three main tenets of this framework were founded in (i) comparisons of absolute exposures (as circulating concentrations or total body burden), (ii) the nature of the toxicity mechanism (i.e., reversible interaction at specific targets versus covalent binding to multiple macromolecules), and (iii) the biological matrix in which the metabolite was observed (circulatory vs excretory). In the present review, this framework is expanded to include a fourth tenet: considerations for the duration of exposure. Basic concepts of pharmacology are utilized to rationalize the relationship between exposure (to parent drug or metabolite) and various effects ranging from desired therapeutic effects through to severe toxicities. Practical considerations of human ADME (absorption-distribution-metabolism-excretion) data, to determine which metabolites should be further evaluated for safety, are discussed. An analysis of recently published human ADME studies shows that the number of drug metabolites considered to be important for MIST can be excessively high if a simple percentage-of-parent-drug criterion is used without consideration of the aforementioned four tenets. Concern over unique human metabolites has diminished over the years as experience has shown that metabolites of drugs in humans will almost always be observed in laboratory animals, although the proportions may vary. Even if a metabolite represents a high proportion of the dose in humans and a low proportion in animals, absolute abundances in animals frequently exceed that in humans because the doses used in animal toxicology studies are much greater than therapeutic doses in humans. The review also updates the enzymatic basis for the differences between species and how these relate to MIST considerations.
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Affiliation(s)
- Dennis A Smith
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer Inc., Sandwich, Kent, UK.
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Dalvie D, Obach RS, Kang P, Prakash C, Loi CM, Hurst S, Nedderman A, Goulet L, Smith E, Bu HZ, Smith DA. Assessment of Three Human in Vitro Systems in the Generation of Major Human Excretory and Circulating Metabolites. Chem Res Toxicol 2009; 22:357-68. [DOI: 10.1021/tx8004357] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deepak Dalvie
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - R. Scott Obach
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Ping Kang
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Chandra Prakash
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Cho-Ming Loi
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Susan Hurst
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Angus Nedderman
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Lance Goulet
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Evan Smith
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Hai-Zhi Bu
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
| | - Dennis A. Smith
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, San Diego California 92121, Pfizer Global Research and Development, Groton Connecticut 06340, and Pfizer Global Research and Development, Sandwich, Kent, United Kingdom
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Shishido Y, Wakabayashi H, Koike H, Ueno N, Nukui S, Yamagishi T, Murata Y, Naganeo F, Mizutani M, Shimada K, Fujiwara Y, Sakakibara A, Suga O, Kusano R, Ueda S, Kanai Y, Tsuchiya M, Satake K. Discovery and stereoselective synthesis of the novel isochroman neurokinin-1 receptor antagonist 'CJ-17,493'. Bioorg Med Chem 2008; 16:7193-205. [PMID: 18640044 DOI: 10.1016/j.bmc.2008.06.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 06/23/2008] [Accepted: 06/24/2008] [Indexed: 10/21/2022]
Abstract
A novel central nervous system (CNS) selective neurokinin-1 (NK(1)) receptor antagonist, (2S,3S)-3-[(1R)-6-methoxy-1-methyl-1-trifluoromethylisochroman-7-yl]-methylamino-2-phenylpiperidine 'CJ-17,493' (compound (+)-1), was synthesized stereoselectively using a kinetic resolution by lipase-PS as a key step. Compound (+)-1 displayed high and selective affinity (K(i)=0.2 nM) for the human NK(1) receptor in IM-9 cells, potent activity in the [Sar(9), Met(O(2))(11)]SP-induced gerbil tapping model (ED(50)=0.04 mg/kg, s.c.) and in the ferret cisplatin (10mg/kg, i.p.)-induced anti-emetic activity model (vomiting: ED(90)=0.07 mg/kg, s.c.), all levels of activity comparable with those of CP-122,721. In addition, compound (+)-1 exhibited linear pharmacokinetics rather than the super dose-proportionality of CP-122,721 and this result provides a potential solution for the clinical issue observed with CP-122,721.
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Affiliation(s)
- Yuji Shishido
- Pfizer Global Research & Development, Nagoya Laboratories, 5-2 Taketoyo, Aichi 470-2394, Japan.
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Scott Obach R, Margolis JM, Logman MJ. In Vitro Metabolism of CP-122,721 ((2S,3S)-2-Phenyl-3-[(5-Trifluoromethoxy-2-Methoxy)Benzylamino]Piperidine), a Non-Peptide Antagonist of the Substance P Receptor. Drug Metab Pharmacokinet 2007; 22:336-49. [DOI: 10.2133/dmpk.22.336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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